In 1995 and 1996, he served as the offensive coordinator at the United States Naval Academy and brought his option offense with him. In 1996, Navy recorded its first winning season in 14 years, going 9–3 with a victory in the Aloha Bowl. Their 9–3 record was the best since 1978 and their 392 points scored were the most in school history up to that point.[6]

Johnson began his head coaching career by returning to Georgia Southern, which he led from 1997 through 2001. During his tenure, the Eagles captured the Division I-AA National Championship twice more in 1999 and 2000, and finished as runner-up in 1998. During his tenure as head coach, they finished with a record of 62–10 (86.1% winning rate).[4]

Johnson is one of only four coaches to record 50 wins in his first four seasons as head coach at the Division I level.[7]

In 2002, Johnson departed Georgia Southern and returned to Navy as head coach. Johnson's initial season saw the Midshipmen win only two of 12 games, though the season ended on a high note with his first victory over Army. Subsequently, Johnson's teams enjoyed a high degree of success.

The 2003 team completed the regular season with an 8–4 mark, including wins over both Air Force and Army, and earned a berth in the Houston Bowl, Navy's first bowl game since 1996. However, the Midshipmen lost to Texas Tech, 38–14. In 2004, Johnson's team posted the program's best record since 1957, finishing the regular season at 9–2 and once again earning a bowl berth, this time in the Emerald Bowl. There Johnson coached the Midshipmen to a win over New Mexico, 34–19, the fifth bowl win in the school's history. The win gave Navy 10 wins on the season, tying a school record that had stood since 1905. For his efforts, Johnson received the Bobby Dodd Coach of the Year Award.

The 2005 Navy squad recorded a mark of 8–4, highlighted by victories over Army, Air Force, and Colorado State in the inaugural Poinsettia Bowl. In 2007, Johnson coached the Midshipmen to their first win over rival Notre Dame since 1963, winning 46–44 in triple-overtime.

Johnson dominated the Commander-in-Chief's Trophy competition, going 11–1 (.917) in his six years, with the only loss against another service academy coming at the hands of Air Force in his first season. He is the only coach in Navy's history to go 6–0 in his first six seasons against Army, and his 2006 senior class was the first in Navy history to win the Commander-in-Chief's Trophy all four of their years.

Much of Johnson's success was predicated on his triple optionflexbone offense, a run-oriented attack that led NCAA Division I-A/FBS football in rushing yards three of his last four years at Navy. Some[who?] have criticized the triple option as gimmick offense unfit for major college football, which may have explained the reluctance of some top programs to offer him a position despite his accomplishments at both Georgia Southern and Navy. Johnson rebutted this argument in numerous press conferences and interviews, asserting that several top teams, including 2005 national championTexas and 2006 national champion Florida, used various forms of the option. In 2008, Johnson told ESPN's Mark Schlabach, "If we can run it against Boston College at Navy, why can't we run it against Boston College at Georgia Tech? If we can beat Pitt with this system at Navy, why can't we beat Pitt at Georgia Tech? Are we going to get worse players at Georgia Tech?"[8]

On December 7, 2007, Johnson accepted the head coaching job at the Georgia Institute of Technology.[1][9] Johnson, who came to Georgia Tech in December after a six-year tenure at Navy, inherited a young roster with reduced numbers because of an NCAA probation. Only 76 players were on scholarship, below the maximum of 85, including three senior walk-ons who were awarded scholarships prior to the start of the season. The roster included 75 freshmen and sophomores; 16 of 22 starters were underclassmen.[1][10]Sports Illustrated predicted Johnson's first Yellow Jacket team would win three games and finish fourth in the Atlantic Coast Conference's Coastal Division.

In 2008, Johnson led the Georgia Tech Yellow Jackets to a 9–4 record.[2] Georgia Tech was 6–1 at home in games played at Bobby Dodd Stadium and 4–2 against ranked opponents, including three wins in November against Florida State, Miami, and Georgia. Georgia Tech, ranked 14th in the BCS standings and 15th in the AP Poll, finished the regular season with a 9–3 record. Though they tied for first place in their division with a 5–3 conference record, the Yellow Jackets failed to advance to the ACC Championship Game by virtue of an early-season loss to eventual ACC champion, Virginia Tech. Georgia Tech accepted a bid to the Chick-Fil-A Bowl, where they were defeated by LSU, 38–3.

Johnson's 2008 Georgia Tech team featured one first-team All-American (Michael Johnson), the ACC Player of the Year (Jonathan Dwyer), and eight first team, second team, and honorable mention All-ACC selections.[11] On December 2, 2008, Johnson was tabbed as ACC Coach of the Year by the Atlantic Coast Sports Media Association (ACSMA). He said, "This is an honor for the football program at Georgia Tech, the coaching staff and the players. There are a lot of great coaches in the ACC, so it's humbling to win such a prestigious honor."[12] Johnson was also named 2008 National Coach of the year by CBSSports.com on the same day.

In 2009, Johnson led the Yellow Jackets to an 11–3 record, including the school's first win at Florida State in school history, and a victory over #4 Virginia Tech in Atlanta, which broke a 17-game home losing streak to top five opponents, and the program's first win over Virginia in Charlottesville since 1990.[13] After a defeat at the hands of Miami in the third week of the season, Georgia Tech won its next eight games, rising as high as #7 in the AP Poll, before losing to unranked rival Georgia in Atlanta to end the regular season. Georgia Tech finished a league-best 7–1 in ACC play and defeated Clemson in the ACC Championship Game for the school's first outright conference championship since 1990. This current title has been vacated by the NCAA for rules violations, which stemmed from what the NCAA described as an isolated instance of former standout wide receiver Demaryius Thomas allegedly receiving $312 in impermissible gifts, and grew to Morgan Burnett allegedly taking gifts and misleading NCAA investigators. Both players denied these allegations and Georgia Tech filed an appeal, which was denied.[14][15][16][17]

Following the end of the regular season, Johnson received ACC Coach of the Year honors for the second consecutive year, becoming the only Georgia Tech head coach in history to win the award in his first two seasons. The Yellow Jackets were paired in the Orange Bowl with the 10th ranked Iowa Hawkeyes. Iowa beat Georgia Tech 24–14, sending Johnson to 0–2 in bowls at Georgia Tech.

In 2010, Georgia Tech started the season ranked 16th in the AP Poll. However, the team suffered a number of high-profile injuries, including to starting quarterback Joshua Nesbitt. The team finished the regular season 6–6 and lost in the Independence Bowl to Air Force 14–7.

In 2011, Johnson has led to the team to its first 6–0 start since 1966 and set a number of school offensive records in the team's 66–24 blowout of Kansas. Johnson proceeded to lose two consecutive games to Virginia and Miami before defeating then #5 Clemson 31–17. The team finished the regular season with an 8–5 record; after losing to Utah in the Sun Bowl on December 31, 2011.

In 2012, Johnson's Yellow Jackets got off to a slow start at 3–5, when then Defensive Coordinator Al Groh was terminated by Johnson. With Charles Kelly coaching the defense thereafter, Georgia Tech won its next three games, and clinched a spot in the 2012 Dr. Pepper ACC Championship game in Charlotte, N.C. Though the Jackets were defeated by Florida State 21–15, the Tech Defense shut out the Seminoles in the second half. GT capped off the season with a 21–7 win over the preseason #1 team in the country, Southern California, in the Hyundai Sun Bowl in El Paso, Texas.

In 2013, Georgia Tech led Georgia 20–0 in the 2nd quarter and 27–17 in the 4th quarter before losing 41–34 in double overtime. The Jackets finished the year 7–6 after a 23–17 loss to Ole Miss in the Music City Bowl.

In 2014, Johnson led Georgia Tech to their fourth Coastal Division title during his tenure and a spot in the 2014 ACC Championship Game. Johnson and the Jackets were predicted to finish 6th in the Coastal division by ESPN in the preseason,[18][19] but again went beyond expectations and achieved a 10-win regular season, 1st place in the Coastal Division, and a 10th place ranking in AP Poll. The Yellow Jackets fell two points short in the ACC title game to the defending national champions, Florida State, but were still selected for their second Orange Bowl berth in six seasons. The season saw the Jackets beat its key rivals Virginia Tech, Miami, Clemson and Georgia. On December 31, 2014, Paul Johnson led the Yellow Jackets to a big win in BCS Orange Bowl. The #12 ranked Yellow Jackets dominated the game in the second half and finished their season with a 49-34 win over the #7 ranked Mississippi State Bulldogs.[20]

^Due to NCAA sanctions, Georgia Tech was forced to vacate all contests won after November 24, 2009 during the 2009 season, which included the ACC Championship victory.[14] The school submitted an appeal of these sanctions on September 9, 2011, which was denied.[15][17]